5EIX

QUINOLONE-STABILIZED CLEAVAGE COMPLEX OF TOPOISOMERASE IV FROM KLEBSIELLA PNEUMONIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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This is version 1.2 of the entry. See complete history


Literature

Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex.

Veselkov, D.A.Laponogov, I.Pan, X.S.Selvarajah, J.Skamrova, G.B.Branstrom, A.Narasimhan, J.Prasad, J.V.Fisher, L.M.Sanderson, M.R.

(2016) Acta Crystallogr D Struct Biol 72: 488-496

  • DOI: 10.1107/S2059798316001212
  • Primary Citation of Related Structures:  
    3RAE, 5EIX

  • PubMed Abstract: 
  • Klebsiella pneumoniae is a Gram-negative bacterium that is responsible for a range of common infections, including pulmonary pneumonia, bloodstream infections and meningitis. Certain strains of Klebsiella have become highly resistant to antibiotics. Despite the vast amount of research carried out on this class of bacteria, the molecular structure of its topoisomerase IV, a type II topoisomerase essential for catalysing chromosomal segregation, had remained unknown ...

    Klebsiella pneumoniae is a Gram-negative bacterium that is responsible for a range of common infections, including pulmonary pneumonia, bloodstream infections and meningitis. Certain strains of Klebsiella have become highly resistant to antibiotics. Despite the vast amount of research carried out on this class of bacteria, the molecular structure of its topoisomerase IV, a type II topoisomerase essential for catalysing chromosomal segregation, had remained unknown. In this paper, the structure of its DNA-cleavage complex is reported at 3.35 Å resolution. The complex is comprised of ParC breakage-reunion and ParE TOPRIM domains of K. pneumoniae topoisomerase IV with DNA stabilized by levofloxacin, a broad-spectrum fluoroquinolone antimicrobial agent. This complex is compared with a similar complex from Streptococcus pneumoniae, which has recently been solved.


    Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, King's College London, 3rd Floor, New Hunt's House, Guy's Campus, London SE1 1UL, England.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit AA, D [auth B], G, J741Klebsiella pneumoniaeMutation(s): 0 
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for R4YHS8 (Klebsiella pneumoniae subsp. rhinoscleromatis SB3432)
Explore R4YHS8 
Go to UniProtKB:  R4YHS8
Find proteins for R4YE07 (Klebsiella pneumoniae subsp. rhinoscleromatis SB3432)
Explore R4YE07 
Go to UniProtKB:  R4YE07
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    SYMMETRISED E-SITE (PRE-CUT)E [auth C], B [auth E], H, K8synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      SYMMETRISED E-SITE (PRE-CUT)F [auth D], C [auth F], I, L12synthetic construct
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.35 Å
      • R-Value Free: 0.259 
      • R-Value Work: 0.224 
      • R-Value Observed: 0.226 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 102.07α = 90
      b = 161.53β = 94.22
      c = 138.6γ = 90
      Software Package:
      Software NamePurpose
      MOSFLMdata reduction
      SCALAdata scaling
      PHASERphasing
      PHENIXrefinement

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K010069/1
      PTC fundingUnited Kingdom--

      Revision History  (Full details and data files)

      • Version 1.0: 2016-04-13
        Type: Initial release
      • Version 1.1: 2016-05-18
        Changes: Database references
      • Version 1.2: 2017-08-30
        Changes: Author supporting evidence, Derived calculations